Combined in vivo and ex vivo three?dimensional (3D) whole?brain imaging of non?transgenic and transgenic animal models holds the promise of novel insights into neural network connectivity patterns. With regard to ex vivo light microscopic imaging of 3D whole?brain datasets, the best approach is brain clearing followed by whole?brain light sheet microscopy (LSM) because of its unique combination of speed, 3D resolving power, and low phototoxicity compared to confocal and multiphoton microscopy. Unlike other methods, the combined brain clearing / LSM approach makes it possible to use intact tissue and retain all intracellular connections within the brain structure. However, LSM systems commercially available are not suitable for ex vivo light microscopic imaging of 3D whole?brain datasets in advanced connectomics research. Recently, Dr. Raju Tomer (Dept. Biol. Sci., Columbia Univ., New York, NY) developed light sheet theta microscopy (LSTM), essentially a unique arrangement of two light sheets oblique to the specimen and one detection objective perpendicular to the specimen. This novel microscope is the basis for a number of capabilities in LSTM that are not all available with any other commercially available LSM systems. The LSTM technology has distinct advantages over confocal and other light sheet microscopes, including the unmatched ability to image thicker tissue specimens over a larger lateral area (XY) at higher optical resolutions, while maintaining fast imaging speed, high imaging quality, and low photo?bleaching. This promising technology serves as the basis for this Lab to Marketplace proposal to develop the ClearScope?, which refines and improves Dr. Tomer's original LSTM system to create a successful commercial microscope for wide?spread adoption. The key technical objectives for developing the ClearScope as a commercial product include creating and testing (i) a ClearScope prototype based on an optimized microscope hardware design; (ii) novel microscope hardware components for the ClearScope, comprising a novel chamber that contains the investigated specimen and the immersion medium, and a novel detection objective changer; (iii) novel control and image acquisition software for the ClearScope; and importantly, (iv) novel software that surpasses the existing state?of?the?art technology to assemble acquired image stacks into large 3D image volumes exceeding 10TB without need to downsample the image information. The production version of the ClearScope will benefit the neuroscience research community, pharmacological and biotechnological R&D, and society in general by improving understanding of neural network connectivity patterns as well as the neuropathological underpinnings of the large?scale connectional alterations associated with human neuropsychiatric and neurological conditions. In particular, this will result in an improved basis for developing novel treatment strategies for complex brain diseases.